Hi John

when you say that they are oriented correctly in freeview, does that mean that they just overlay properly on the volume? Or that e.g. what freeview thinks is anterior is actually anterior, etc...?

cheers Bruce

On Mon, 29 Feb 2016, John Plass wrote:

Hello Freesurfer Experts, I wrote in recently about my parcellation troubles with an ex-vivo scan (link). Digging further, I've found that the surfaces I've produced following the Ex-Vivo recon instructions are oriented properly when viewed in freeview (freeview -v mri/orig.mgz -f surf/rh.white:edgecolor=blue surf/rh.pial:edgecolor=red), but are misoriented in tkmedit (tkmedit $SUBID orig.mgz rh.white). I suspect that something related this might be the source of the parcellation problems. Any idea why this might be and how I can fix it?

Relevant background information: *volumes were reoriented before FS processing using the command "mri_convert -c -iid 0 -1 0 -ijd 0 0 -1 -ikd 1 0 0 mprage.nii.gz  mprage.mgz" *running freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 on Ubuntu 14.04

As always, I'm very grateful for any help you can provide.

John